StarScan: a web server for scanning small RNA targets from degradome sequencing data.

Shun Liu,Liang-Hu Qu,Ke-Ren Zhou,Jun-Hao Li,Jian-Hua Yang,Jie Wu,Hui Zhou

doi:10.1093/nar/gkv524

Abstract

Endogenous small non-coding RNAs (sRNAs), including microRNAs, PIWI-interacting RNAs and small interfering RNAs, play important gene regulatory roles in animals and plants by pairing to the protein-coding and non-coding transcripts. However, computationally assigning these various sRNAs to their regulatory target genes remains technically challenging. Recently, a high-throughput degradome sequencing method was applied to identify biologically relevant sRNA cleavage sites. In this study, an integrated web-based tool, StarScan (sRNA target Scan), was developed for scanning sRNA targets using degradome sequencing data from 20 species. Given a sRNA sequence from plants or animals, our web server performs an ultrafast and exhaustive search for potential sRNA–target interactions in annotated and unannotated genomic regions. The interactions between small RNAs and target transcripts were further evaluated using a novel tool, alignScore. A novel tool, degradomeBinomTest, was developed to quantify the abundance of degradome fragments located at the 9–11th nucleotide from the sRNA 5′ end. This is the first web server for discovering potential sRNA-mediated RNA cleavage events in plants and animals, which affords mechanistic insights into the regulatory roles of sRNAs. The StarScan web server is available at http://mirlab.sysu.edu.cn/starscan/.

Highlights

Eukaryotic genomes encode thousands of small non-coding RNAs, such as microRNAs, PIWIinteracting RNAs and endogenous small interfering RNAs [1,2,3,4,5]
After surveying the alignments of experimentally validated miRNA–target interactions (MTIs) in the reference set (Supplementary Table S1), we found that most of them (119 of 121) presented just one mismatch in a > = 10 nt stretch of a miRNA–target duplex
To predict targets and their cleavage sites, we developed a novel tool, alignScore, to evaluate alignments between sRNAs and targets using a proven scoring schema with some modifications and to determine if the cleavage sites of targets were at the sRNA positions 9, 10 and 11 in plants and animals [9,30,31,32]

Summary

Introduction

Eukaryotic genomes encode thousands of small non-coding RNAs (sRNAs), such as microRNAs (miRNAs), PIWIinteracting RNAs (piRNAs) and endogenous small interfering RNAs (endo-siRNAs) [1,2,3,4,5]. In addition to being able to analyze plant miRNA targets as with existing tools, our web server can predict targets of diverse animal sRNAs including miRNAs, piRNAs and endo-siRNAs. StarScan was designed to search for small RNA targets in annotated and unannotated genomic regions.

Results

Conclusion